I've installed throttle body spacers many times with after market intakes. It makes things a bit tight but with the elbows you usually have room for adjustment. I typically use Airaid or something that puts a "spin" on the air.

Honestly it should be one of your last mods. Make sure you have good flow for exhaust and intake and your 02 sensors are changed at the proper interval. After all that, then add the spacer. Seems mid range response is better, in theory because the intake manifold volume is increased marginally. I would focus on the other stuff first though if MPG is your goal. Also make sure your tire pressure is to spec.